<% String title="DAS - interaction";
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<p>
This page is part of the <a href="spec_1.53E.jsp">DAS 1.53E specification</a>
</p>

<h2>Molecular interaction extension</h2>

<b>Request:</b> interaction command

<br/>

<b>Version:</b> 2008/10/31

<br/>

<b>Authors:</b> <a href="mailto:hagen.blankenburg@mpi-inf.mpg.de">Hagen Blankenburg</a>, Robert D. Finn, Andreas Prlic, Andrew Jenkinson, Mario Albrecht

<br/>

<b>Scope:</b> DASMI Server

<br/>

<b>Command:</b> interaction

<br/>

<b>Format:</b>
<pre>

PREFIX/das/DATASOURCE/interaction?interactor=ID
	[;interactor=ID]
	[;operation=INTERSECTION_UNION]
	[;detail=[ref:ID,]property:A_PROPERTY]
	[;detail=[ref:ID,]property:A_PROPERTY,value:A_VALUE]
	
</pre>

<b>Description:</b> This section describes how a user or DAS client can request data from
a <strong>DASMI</strong> server. The new DAS command for requesting interactions
is named <i>interaction</i> and provides additional query parameters of three types, <i>interactor</i>,
<i>operation</i>, and <i>detail</i>. The syntax of the interaction command is shown below.
<br/>
<br/>
<b>Arguments:</b>
An <i><b>interactor</b></i> parameter represents an identifier
of the target interactor. One or several <i>interactor</i>
parameters can be provided. If only one <i>interactor</i>
parameter is present, all available interaction partners
of this interactor shall be returned. <br/>
The optional <i><b>operation</b></i> parameter can be used once
for defining the response type if more than one
<i>interactor</i> parameter is provided. If <i>operation</i>
is not provided or has the value <i>intersection</i>, the interaction
partners that interact with all query interactors
shall be returned. If <i>operation</i> has the value
<i>union</i>, the interactions for each of the query
interactors shall be returned. <br/>
The <i><b>detail</b></i> parameter can be used to refine a query further. 
If the optional <i>ref</i> attribute is used, it indicates that the  
detail (e.g. an experimental role) is linked to the interactor with  
the same ID, if it is ommited the detail (e.g. a literature reference) 
is linked to the interation. A detail can be described in two 
different ways. The short form <i>detail=property:A_PROPERTY</i>
will return all interactions for which the value of a certain property 
is present, regardless of what the value of that property is. 
In contrast, the long form <i>detail=property:A_PROPERTY,value:A_VALUE</i> 
will return all interactions for which a certain property is present and has a
specific value. For example, while the short form allows
for retrieving all interactions which possess a
confidence score or a literature reference, the long form effects the retrieval
of only those interactions for which that confidence
score or literature reference has a specific value.

<br/>

<b>Examples:</b>

<pre>
.../das/DSN/interaction?interactor=3406
</pre>
The simplest form of the interaction command is a request with exactly one
interactor parameter. This query retrieves all interactions reported for the
interactor with the Entrez Gene identifier 3406.

<pre>
.../das/DSN/interaction?interactor=PF00121&detail=property:confidenceScore
</pre>
This query returns all interactions reported for the domain interactor with the Pfam identifier PF00121,
where a confidence score (regardless of the value of that score) has been assigned.

<pre>
.../das/DSN/interaction?interactor=P38330</br>
	&detail=ref:P38330,property:experimentalRole,value:bait
</pre>	
This query returns all interactions, where the protein interactor with the UniProt accession number P38330 has
been used in the experimental role of a bait.

<pre>
.../das/DSN/interaction?interactor=P52597&interactor=P60010
</pre>
This query returns all interactions, where both protein interactors P52597
and P60010 are participating.

<pre>
.../das/DSN/interaction?interactor=P52597&interactor=P60010</br>
	&operation=UNION
</pre>
Unlike the query above, this query returns all interactions, where either the protein interactor P52597 or the interactor
P60010 are participating.

<pre>
.../das/DSN/interaction?interactor=P38330;interactor=P32324;</br>
	interactor=P10591;interactor=P16140
</pre>
This exemplary query returns all protein complexes, where the four proteins P38330,
P32324, P10591, and P16140 are participating.

<pre>
.../interaction?interactor=P38330&interactor=P38332</br>
	&detail=property:confidenceScore</br>
	&detail=ref:P38330,property:experimentalRole,value:bait</br>
	&detail=ref:P28332,property:experimentalRole,value:prey 
</pre>
This query would return all interactions, where the protein P38330 was used as a bait, 
P38332 was used as a prey, and a confidence score is available for the interaction.

<br/>
<br/>

<b>Response:</b> DASINT XML format
This section defines the DASMI server response. The document returned from an
interaction request is a DASINT XML document. Due to several optional elements
and attributes, the complexity of the DASINT XML format may vary significantly.

<br/>

Listing 1 shows the plainest possible form; Listing 2 shows the form fully utilizing all
elements.
<br/>

<center>Listing 1: Plainest possible DASINT XML format.</center>
<pre id="framed">
&lt;DASINT xmlns:xsi="xsd namespace" xmlns="namespace" 
	xsi:schemaLocation="schema location" &gt;
	&lt;INTERACTOR intId="id" shortLabel="name" dbSource="source" 
		dbAccessionId="acc" dbCoordSys="cs"/&gt;
	&lt;INTERACTION name="name" dbSource="source" dbAccessionId="acc"&gt;
		&lt;PARTICIPANT intId="id"/&gt;
		&lt;PARTICIPANT intId="id"/&gt;
	&lt;/INTERACTION&gt;
&lt;/DASINT&gt;
</pre>

<br/>

<center>Listing 2: Completely utilized DASINT XML format.</center>

<pre id="framed">
&lt;DASINT xmlns:xsi=&quot;xsd namespace&quot; xmlns=&quot;namespace&quot;
xsi:schemaLocation=&quot;schema location&quot; &gt;

&lt;INTERACTOR intId=&quot;id&quot; shortLabel=&quot;name&quot; dbSource=&quot;source&quot;
	dbSourceCvId=&quot;cv id&quot; dbVersion=&quot;version&quot;
	dbAccessionId=&quot;acc&quot; dbCoordSys=&quot;cs&quot;&gt;

	&lt;DETAIL property=&quot;interactor property&quot; value=&quot;a value&quot;
		propertyCvId=&quot;cv id&quot; valueCvId=&quot;cv id&quot;&gt;
		&lt;RANGE start=&quot;x&quot; end=&quot;y&quot; startStatus=&quot;status&quot;
			endStatus=&quot;status&quot; startStatusCvId=&quot;cv id&quot;
			endStatusCvId=&quot;cv id&quot;/&gt;
	&lt;/DETAIL&gt;

	&lt;SEQUENCE start=&quot;x&quot; end=&quot;y&quot;&gt;SEQUENCESEQUENCE&lt;/SEQUENCE&gt;

&lt;/INTERACTOR&gt;

&lt;INTERACTION name=&quot;name&quot; dbSource=&quot;source&quot; dbSourceCvId=&quot;cv id&quot; 
	dbVersion=&quot;version&quot; dbAccessionId=&quot;acc&quot;&gt;

	&lt;DETAIL property=&quot;interaction property&quot; value=&quot;a value&quot;
		propertyCvId=&quot;cv id&quot; valueCvId=&quot;cvid&quot;&gt;

		&lt;PARTICIPANT intId=&quot;id&quot;&gt;	
			&lt;DETAIL property=&quot;participant property&quot; value=&quot;a value&quot;
					propertyCvId=&quot;cv id&quot; valueCvId=&quot;cv id&quot;&gt;
				&lt;RANGE start=&quot;x&quot; end=&quot;y&quot; startStatus=&quot;status&quot;
					endStatus=&quot;status&quot; startStatusCvId=&quot;cv id&quot;
					endStatusCvId=&quot;cv id&quot;/&gt;
			&lt;/DETAIL&gt;
		&lt;/PARTICIPANT&gt;

		&lt;PARTICIPANT intId=&quot;id&quot;&gt;
			&lt;DETAIL property=&quot;participant property&quot; value=&quot;a value&quot;
				propertyCvId=&quot;cv id&quot; valueCvId=&quot;cv id&quot;&gt;
			&lt;RANGE start=&quot;x&quot; end=&quot;y&quot; startStatus=&quot;status&quot;
				endStatus=&quot;status&quot; startStatusCvId=&quot;cv id&quot;
				endStatusCvId=&quot;cv id&quot;/&gt;
			&lt;/DETAIL&gt;
		&lt;/PARTICIPANT&gt;
&lt;/INTERACTION&gt;
&lt;/DASINT&gt;
</pre>

<h3>DASINT XML Schema Definition</h3>
<p>
An XML Schema defines the structure of an XML document, that is, the order,
hierarchy, cardinality and type of its elements. An overview of the DASINT XML
Schema Definition is shown in Figure 1.
</p>

<center>Figure 1: DASINT XML Schema Definition.</center>

<img src="img/interactionDAS.png" width="532" height="158" ALT="DASINT XML Schema"/>

<br/>

<b>Format:</b>
<%@ include file="sangertablestart.jsp" %>

<tr id="row1">
<td>
&lt;DASINT&gt; (required; one)</td>
<td>
The root element of the DASINT XML format is merely an outer envelope.
The attribute xmlns:xsi indicates the official XML schema instance
namespace. The attributes xmlns and xsi:schemaLocation define the
DASINT namespace and the location of the DASINT XML Schema
Definition, respectively.
</td>
</tr>

<tr id="row2">
<td>
	&lt;INTERACTOR&gt; (required; one or more)
	</td>
<td>
Each interactor, participating in an interaction, has to be initially defined
within an INTERACTOR element. The INTERACTOR element thereby contains
general, i.e., interaction independent, information on the interactor. The
mandatory attributes shortLabel, dbSource, dbAccessionId and
dbCoordSys define the origin and the identity of the interactor. The optional
dbSourceCvId and dbVersion can be used to define the source database in
more detail. The internal linkage between the interactor definition and its
occurrence as a participant within an interaction is enabled with the intId
attribute.
</td>
</tr>

<tr id="row1">
<td>
	&lt;INTERACTION&gt; (required; one or more)
	</td>
<td>	
Being the central element within the DASINT protocol, each INTERACTION
element represents one interaction. The mandatory attributes name, dbSource
and dbAccessionId define the origin of the interaction. The optional
dbSourceCvId and dbVersion can be used to further define the source
database.
</td>
</tr>

<tr id="row2">
<td>&lt;PARTICIPANT&gt; (required; two or more)
</td>
<td>
A participant is an interactor participating in an interaction. The participant
can have additional, interaction dependent, features such as experimental role
or binding sites. The linkage to the initial interactor definition is enabled
through the sole attribute intId.
</td>
</tr>

<tr id="row1">
<td>&lt;SEQUENCE&gt; (optional; zero or one per INTERACTOR)</td>
<td>
The SEQUENCE element contains the sequence of the interactor. The type of
the sequence, for instance, nucleotide or protein, is defined through the
coordinate system of the interactor. The optional attributes start and end
can be used to limit the sequence.
</td>

<tr id="row2">
<td>&lt;DETAIL&gt; (optional; zero or more per INTERACTOR, PARTICIPANT or
INTERACTION)</td>
<td>
The DETAIL element is the central element for providing additional
information for the interactor, its role as a participant or an interaction.
Depending on the father element, the detail is assigned to either one of these.
To allow the element to contain all kinds of information, the mandatory
attribute combination property and value is defined. To further define the
property and the value through controlled vocabularies, the optional attributes
propertyCvId and valueCvId can be used in addition.
</td>
</tr>


<tr id="row1">
<td>&lt;RANGE&gt; (optional; zero or more per DETAIL)</td>
<td>The optional RANGE element may be used to limit a DETAIL to a certain
position on the sequence of an interactor. If it is used, the mandatory start
and end attributes define the associated stretch of the sequence. The optional
startStatus and endStatus can be used to define the respective position
more detailed with terms like &quot;less than&quot; or &quot;greater than&quot;. To define these
terms with controlled vocabulary terms, the attributes startStatusCvId and
endStatusCvId can be used. Since an interaction does not have a sequence,
the RANGE element may only be used within DETAIL elements that are child
elements of either the INTERACTOR or the PARTICIPANT element.
</td>
</tr>

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<br/>
<b>Examples</b><br/>
The two following listings show potential applications of the DASINT XML format.
The former Listing 3 describes a domain-domain interaction between two Pfam
domains. The only additional information, besides the pure interaction information, is
a confidence score assigned to the INTERACTION element. The latter Listing 4
represents a protein-protein interaction between two UniProt proteins and is far more
detailed. It provides additional information for the interactor in general, its role as a
participant, and the interaction.

<center>Listing 3: DASINT XML representing a domain-domain interaction between two
Pfam domains. As an additional detail, a confidence score has been
assigned to the interaction.</center>

<pre id="framed">
&lt;?xml version=&quot;1.0&quot; encoding=&quot;UTF-8&quot;?&gt;

&lt;DASINT xmlns:xsi=&quot;http://www.w3.org/2001/XMLSchema-instance&quot;
		xmlns=&quot;http://dasmi.de/&quot;
		xsi:schemaLocation=&quot;http://dasmi.de/ http://dasmi.de/dasint.xsd&quot; &gt;

	&lt;INTERACTOR intId=&quot;1&quot; shortLabel=&quot;Clp N&quot; dbSource=&quot;Pfam&quot;
		dbSourceCvId=&quot;MI:0451&quot; dbVersion=&quot;20&quot;
		dbAccessionId=&quot;PF02861&quot; dbCoordSys=&quot;Pfam,Protein Sequence&quot;/&gt;
		
	&lt;INTERACTOR intId=&quot;2&quot; shortLabel=&quot;AAA&quot; dbSource=&quot;Pfam&quot;
		dbSourceCvId=&quot;MI:0451&quot; dbVersion=&quot;20&quot;
		dbAccessionId=&quot;PF00004&quot; dbCoordSys=&quot;Pfam,Protein Sequence&quot;/&gt;

	&lt;INTERACTION name=&quot;AAA-Clp N&quot; dbSource=&quot;ldsc&quot; dbAccessionId=&quot;&quot;&gt;
		&lt;DETAIL property=&quot;confidenceScore&quot; value=&quot;38.0376&quot;/&gt;
		&lt;PARTICIPANT intId=&quot;1&quot;/&gt;
		&lt;PARTICIPANT intId=&quot;2&quot;/&gt;
	&lt;/INTERACTION&gt;

&lt;/DASINT&gt;
</pre>


<center>
Listing 4: DASINT XML representing a protein-protein interaction between two
UniProt proteins. Several additional details have been assigned to the
interactor, the participant, and the interaction. Note that the SEQUENCE
has been stripped.
</center>

<pre id="framed">
&lt;?xml version=&quot;1.0&quot; encoding=&quot;UTF-8&quot;?&gt;
&lt;DASINT xmlns:xsi=&quot;http://www.w3.org/2001/XMLSchema-instance&quot;
		xmlns=&quot;http://dasmi.de/&quot;
		xsi:schemaLocation=&quot;http://dasmi.de/ http://dasmi.de/dasint.xsd&quot; &gt;

	&lt;INTERACTOR intId=&quot;1&quot; shortLabel=&quot;exo1 human&quot;
		dbSource=&quot;uniprotkb&quot; dbSourceCvId=&quot;MI:0486&quot;
		dbAccessionId=&quot;Q9UQ84&quot; dbVersion=&quot;SP 26&quot;
		dbCoordSys=&quot;UniProt,Protein Sequence&quot;&gt;
		&lt;DETAIL property=&quot;type&quot; value=&quot;protein&quot;
			valueCvId=&quot;MI:0326&quot;/&gt;
		&lt;SEQUENCE start=&quot;1&quot; end=&quot;846&quot;&gt;MGIQGLLK[..]KPECIFQ&lt;/SEQUENCE&gt;
	&lt;/INTERACTOR&gt;

	&lt;INTERACTOR intId=&quot;2&quot; shortLabel=&quot;msh2 human&quot;
		dbSource=&quot;uniprotkb&quot; dbSourceCvId=&quot;MI:0486&quot;
		dbAccessionId=&quot;P43246&quot; dbVersion=&quot;SP 59&quot;
		dbCoordSys=&quot;UniProt,Protein Sequence&quot;&gt;
	
		&lt;DETAIL property=&quot;type&quot; value=&quot;protein&quot;
			valueCvId=&quot;MI:0326&quot;/&gt;
		&lt;SEQUENCE start=&quot;1&quot; end=&quot;934&quot;&gt;MAVQPKEQ[..]REVFKT&lt;/SEQUENCE&gt;
	&lt;/INTERACTOR&gt;

	&lt;INTERACTION name=&quot;exo1-msh2&quot; dbSource=&quot;mint&quot;
		dbSourceCvId=&quot;MI:0471&quot; dbAccessionId=&quot;MINT-16442&quot;
		dbVersion=&quot;2006-04-14&quot;&gt;
		&lt;DETAIL property=&quot;type&quot; propertyCvId=&quot;MI:0190&quot;
			value=&quot;aggregation&quot; valueCvId=&quot;MI:0191&quot;/&gt;
		&lt;PARTICIPANT intId=&quot;1&quot;&gt;
			&lt;DETAIL property=&quot;bindingSite&quot; propertyCvId=&quot;MI:0117&quot;
				value=&quot;&quot;&gt;
				&lt;RANGE start=&quot;604&quot; end=&quot;846&quot;/&gt;
			&lt;/DETAIL&gt;

			&lt;DETAIL property=&quot;experimentalRole&quot;
				propertyCvId=&quot;MI:0495&quot; value=&quot;bait&quot;
				valueCvId=&quot;MI:0496&quot;/&gt;
		&lt;/PARTICIPANT&gt;

		&lt;PARTICIPANT intId=&quot;2&quot;&gt;
			&lt;DETAIL property=&quot;bindingSite&quot; propertyCvId=&quot;MI:0117&quot;
				value=&quot;&quot;&gt;
				&lt;RANGE start=&quot;601&quot; end=&quot;671&quot;/&gt;
			&lt;/DETAIL&gt;
			&lt;DETAIL property=&quot;experimentalRole&quot;
				propertyCvId=&quot;MI:0495&quot; value=&quot;prey&quot;
				valueCvId=&quot;MI:0498&quot;/&gt;
		&lt;/PARTICIPANT&gt;
	&lt;/INTERACTION&gt;
&lt;/DASINT&gt;
</pre>

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